bhklab/pharmacogx issues and pull requests

#120 - Incorporate Synergy Score Calculations from https://github.com/bhklab/PharmacoGx-private/blob/master/R/predictResponse.R Into CoreGx

Issue - State: closed - Opened by ChristopherEeles about 3 years ago - 2 comments
Labels: enhancement

#120 - Incorporate Synergy Score Calculations from https://github.com/bhklab/PharmacoGx-private/blob/master/R/predictResponse.R Into CoreGx

Issue - State: closed - Opened by ChristopherEeles about 3 years ago - 2 comments
Labels: enhancement

#100 - Minor documentation tweaks

Pull Request - State: closed - Opened by allaway almost 3 years ago - 4 comments
Labels: enhancement

#100 - Minor documentation tweaks

Pull Request - State: closed - Opened by allaway almost 3 years ago - 4 comments
Labels: enhancement

#99 - Unable to load CMap data

Issue - State: closed - Opened by iditkosti about 3 years ago - 7 comments

#98 - Merge development into master

Pull Request - State: closed - Opened by ChristopherEeles about 3 years ago

#98 - Merge development into master

Pull Request - State: closed - Opened by ChristopherEeles about 3 years ago

#96 - Problem with intersectPSets

Issue - State: open - Opened by bhaibeka over 3 years ago - 10 comments
Labels: bug

#96 - Problem with intersectPSets

Issue - State: open - Opened by bhaibeka over 3 years ago - 10 comments
Labels: bug

#95 - Beat AML and Smiles missing

Issue - State: closed - Opened by SafiaSafa over 3 years ago - 5 comments

#94 - Issue with availablePSets(): 'Error in open.connection(con, "rb") : HTTP error 500'

Issue - State: closed - Opened by Pedramto89 over 3 years ago - 15 comments

#93 - AAC and AUC values are the same

Issue - State: open - Opened by islic over 3 years ago - 6 comments

#93 - AAC and AUC values are the same

Issue - State: open - Opened by islic over 3 years ago - 6 comments

#92 - The Range of ic50_recomputed

Issue - State: closed - Opened by AlirezaShokrollahi over 3 years ago - 2 comments

#91 - pretty much self explanatory, as far as I can see the fdr column shouldn't have been added there

Pull Request - State: closed - Opened by p-smirnov over 3 years ago

#91 - pretty much self explanatory, as far as I can see the fdr column shouldn't have been added there

Pull Request - State: closed - Opened by p-smirnov over 3 years ago

#90 - PharmacoGx and ggplot2 function conflict?

Issue - State: closed - Opened by DGendoo over 3 years ago - 9 comments

#90 - PharmacoGx and ggplot2 function conflict?

Issue - State: closed - Opened by DGendoo over 3 years ago - 9 comments

#89 - A progress bar for drugSensitivitySig() would be nice as it can take a long time to compute

Issue - State: open - Opened by bhaibeka over 3 years ago - 1 comment
Labels: enhancement

#88 - No documentation for geneDrugSensitivity()

Issue - State: closed - Opened by bhaibeka over 3 years ago
Labels: enhancement

#87 - Fix: #84, misplaced bracket in drugDoseResponseCurve.R

Pull Request - State: closed - Opened by ChristopherEeles over 3 years ago - 1 comment

#87 - Fix: #84, misplaced bracket in drugDoseResponseCurve.R

Pull Request - State: closed - Opened by ChristopherEeles over 3 years ago - 1 comment

#86 - inconsistency between sensitivityProfiles() and computeAUC()

Issue - State: open - Opened by bhaibeka over 3 years ago
Labels: enhancement

#86 - inconsistency between sensitivityProfiles() and computeAUC()

Issue - State: open - Opened by bhaibeka over 3 years ago
Labels: enhancement

#85 - units must be enforced and/or documented

Issue - State: open - Opened by bhaibeka over 3 years ago - 1 comment
Labels: enhancement

#85 - units must be enforced and/or documented

Issue - State: open - Opened by bhaibeka over 3 years ago - 1 comment
Labels: enhancement

#84 - Error in drugDoseResponseCurve.R

Issue - State: closed - Opened by bhaibeka over 3 years ago - 1 comment
Labels: bug

#83 - Create a computeAAC function

Issue - State: open - Opened by bhaibeka over 3 years ago
Labels: enhancement

#82 - Inconsistencies in drug names?

Issue - State: open - Opened by bhaibeka over 3 years ago - 7 comments

#82 - Inconsistencies in drug names?

Issue - State: open - Opened by bhaibeka over 3 years ago - 7 comments

#81 - What to do with PharmacoGx:::.summarizeSensitivityNumbers

Issue - State: open - Opened by p-smirnov over 3 years ago - 1 comment
Labels: question

#81 - What to do with PharmacoGx:::.summarizeSensitivityNumbers

Issue - State: open - Opened by p-smirnov over 3 years ago - 1 comment
Labels: question

#80 - "Gender" in cellInfo should be replaced by "Sex" in all PSets

Issue - State: closed - Opened by bhaibeka over 3 years ago - 1 comment

#80 - "Gender" in cellInfo should be replaced by "Sex" in all PSets

Issue - State: closed - Opened by bhaibeka over 3 years ago - 1 comment

#79 - Where did the raw viability data for CCLE was retrieved and what normalization steps were performed on the raw viability values ?

Issue - State: closed - Opened by Durdam over 3 years ago - 2 comments

#79 - Where did the raw viability data for CCLE was retrieved and what normalization steps were performed on the raw viability values ?

Issue - State: closed - Opened by Durdam over 3 years ago - 2 comments

#78 - Error creating new PharmacoSet

Issue - State: closed - Opened by kevincjnixon over 3 years ago - 4 comments

#77 - summarizeSensitivityProfiles not working after update

Issue - State: closed - Opened by FarzanT over 3 years ago - 2 comments

#77 - summarizeSensitivityProfiles not working after update

Issue - State: closed - Opened by FarzanT over 3 years ago - 2 comments

#76 - normalization method of RNA-Seq data

Issue - State: closed - Opened by zhumengyan almost 4 years ago - 2 comments

#76 - normalization method of RNA-Seq data

Issue - State: closed - Opened by zhumengyan almost 4 years ago - 2 comments

#75 - Check on wrong assay?

Issue - State: open - Opened by p-smirnov almost 4 years ago - 3 comments

#74 - CTRP data set issue with latest PharmacoGx version (2.3.5)

Issue - State: closed - Opened by hmkim almost 4 years ago - 2 comments

#73 - Looking for Precompiled CMAP and L1000 data for v.2.2.0

Issue - State: open - Opened by Swilson6 almost 4 years ago - 13 comments

#72 - creating a pharmacoset

Issue - State: closed - Opened by lovenicole about 4 years ago - 8 comments

#72 - creating a pharmacoset

Issue - State: closed - Opened by lovenicole about 4 years ago - 8 comments

#71 - Mutation data all "1" for gCSI_2017 using either summary.stat

Issue - State: open - Opened by khughitt about 4 years ago - 5 comments

#71 - Mutation data all "1" for gCSI_2017 using either summary.stat

Issue - State: open - Opened by khughitt about 4 years ago - 5 comments

#70 - error in checkPsetStructure

Issue - State: closed - Opened by spocks about 4 years ago - 2 comments

#70 - error in checkPsetStructure

Issue - State: closed - Opened by spocks about 4 years ago - 2 comments

#69 - Problem with downloading GDSC_2019(v2-8.0) on Windows only.

Issue - State: closed - Opened by p-smirnov over 4 years ago - 11 comments

#68 - Updating development with the bug patches from master/release

Pull Request - State: closed - Opened by p-smirnov over 4 years ago

#67 - adding correction for summarizing pertubation datasets

Pull Request - State: closed - Opened by p-smirnov over 4 years ago - 1 comment

#67 - adding correction for summarizing pertubation datasets

Pull Request - State: closed - Opened by p-smirnov over 4 years ago - 1 comment

#66 - Available PSets data.frame formatting

Issue - State: open - Opened by ChristopherEeles over 4 years ago
Labels: bug

#66 - Available PSets data.frame formatting

Issue - State: open - Opened by ChristopherEeles over 4 years ago
Labels: bug

#65 - Core gx dependency

Pull Request - State: closed - Opened by ChristopherEeles over 4 years ago

#64 - Core gx dependency

Pull Request - State: closed - Opened by ChristopherEeles over 4 years ago

#63 - Added download from Zenodo functions. Currently broken on Orcestra side for some PSets, working on the fixes.

Pull Request - State: closed - Opened by p-smirnov over 4 years ago

#63 - Added download from Zenodo functions. Currently broken on Orcestra side for some PSets, working on the fixes.

Pull Request - State: closed - Opened by p-smirnov over 4 years ago

#62 - New plots

Pull Request - State: closed - Opened by p-smirnov over 4 years ago - 1 comment

#62 - New plots

Pull Request - State: closed - Opened by p-smirnov over 4 years ago - 1 comment

#61 - CMap update

Issue - State: open - Opened by ZKorda almost 5 years ago

#61 - CMap update

Issue - State: open - Opened by ZKorda almost 5 years ago

#60 - Cell line metadata incorrectly processed

Issue - State: open - Opened by khughitt almost 5 years ago - 2 comments

#60 - Cell line metadata incorrectly processed

Issue - State: open - Opened by khughitt almost 5 years ago - 2 comments

#59 - summarizeSensitivityProfiles drug parameter does not work when drug was not tested.

Issue - State: open - Opened by p-smirnov almost 5 years ago

#58 - How to use drugSensitivitySig function to discover drug for gene

Issue - State: open - Opened by TINGJINJANE about 5 years ago

#57 - drugDoseResponseCurve needs a space after the legend label

Issue - State: open - Opened by p-smirnov over 5 years ago

#57 - drugDoseResponseCurve needs a space after the legend label

Issue - State: open - Opened by p-smirnov over 5 years ago

#56 - summarizeSensitivityProfiles returns same values for both AAC and auc

Issue - State: open - Opened by soheilj over 5 years ago

#56 - summarizeSensitivityProfiles returns same values for both AAC and auc

Issue - State: open - Opened by soheilj over 5 years ago

#55 - InterectPSets still doesnt do the right thing on concentrations?

Issue - State: open - Opened by p-smirnov over 5 years ago - 1 comment

#55 - InterectPSets still doesnt do the right thing on concentrations?

Issue - State: open - Opened by p-smirnov over 5 years ago - 1 comment

#54 - summarizeMolecularProfiles returns missing values while fill.missing is set to FALSE

Issue - State: open - Opened by soheilj over 5 years ago

#54 - summarizeMolecularProfiles returns missing values while fill.missing is set to FALSE

Issue - State: open - Opened by soheilj over 5 years ago

#53 - Error intersecting CCLE and CTRPv2

Issue - State: open - Opened by soheilj over 5 years ago - 6 comments

#53 - Error intersecting CCLE and CTRPv2

Issue - State: open - Opened by soheilj over 5 years ago - 6 comments

#52 - ic50 published values & Transformation to get recomputed values?

Issue - State: open - Opened by e-arslan over 5 years ago - 1 comment

#52 - ic50 published values & Transformation to get recomputed values?

Issue - State: open - Opened by e-arslan over 5 years ago - 1 comment

#51 - Error when intersecting PSets and plotting dose response curves

Issue - State: closed - Opened by FarzanT over 5 years ago - 2 comments

#51 - Error when intersecting PSets and plotting dose response curves

Issue - State: closed - Opened by FarzanT over 5 years ago - 2 comments

#50 - can't reproduce the result of case study 2 from publication

Issue - State: closed - Opened by yeaouh over 5 years ago - 1 comment

#50 - can't reproduce the result of case study 2 from publication

Issue - State: closed - Opened by yeaouh over 5 years ago - 1 comment

#49 - Add warnings when users try to compare data from different processing

Issue - State: open - Opened by p-smirnov over 5 years ago

#49 - Add warnings when users try to compare data from different processing

Issue - State: open - Opened by p-smirnov over 5 years ago

#48 - sessionInfo() during package installation (will) capture an incorrect path

Issue - State: closed - Opened by mtmorgan over 5 years ago - 1 comment

#48 - sessionInfo() during package installation (will) capture an incorrect path

Issue - State: closed - Opened by mtmorgan over 5 years ago - 1 comment

#47 - Issue with ordering doses in drugDoseResponseCurve

Issue - State: open - Opened by sisiranair almost 6 years ago - 2 comments

#47 - Issue with ordering doses in drugDoseResponseCurve

Issue - State: open - Opened by sisiranair almost 6 years ago - 2 comments

#46 - can't subset CTRPv2

Issue - State: open - Opened by spocks over 6 years ago - 1 comment

#46 - can't subset CTRPv2

Issue - State: open - Opened by spocks over 6 years ago - 1 comment

#45 - documentation error in summarizeSensitivityProfiles

Issue - State: open - Opened by spocks over 6 years ago - 1 comment

#45 - documentation error in summarizeSensitivityProfiles

Issue - State: open - Opened by spocks over 6 years ago - 1 comment

#44 - Is retrieval of connectivity at cell line level possible?

Issue - State: open - Opened by elenichri over 6 years ago

#44 - Is retrieval of connectivity at cell line level possible?

Issue - State: open - Opened by elenichri over 6 years ago

#43 - Expression data in CTRPv2 PSet

Issue - State: closed - Opened by MomenehForoutan almost 7 years ago - 20 comments

#43 - Expression data in CTRPv2 PSet

Issue - State: closed - Opened by MomenehForoutan almost 7 years ago - 20 comments

#42 - Map drug IDs and drug names in GDSC1000 PSet

Issue - State: closed - Opened by MomenehForoutan almost 7 years ago - 1 comment

#42 - Map drug IDs and drug names in GDSC1000 PSet

Issue - State: closed - Opened by MomenehForoutan almost 7 years ago - 1 comment

GitHub / bhklab/pharmacogx issues and pull requests